Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HMGB1

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Normal lung fibroblast IMR90
cell line
IMR90
condition
Proliferating
chip antibody
HMGB1 Hybridoma Ab (PCRP-HMGB1-4F10)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
~25 million cells per sample were double crosslinked in EGS/PFA and processed with ChIP-IT high sensitivity kit (Active motif) as per manufacturer instructions. Immunoprecipitation was carried out with 4 ug of HMGB1 antibody (Hybridoma, PCRP-HMGB1-4F10) in 30 ug of chromatin. DNA was purified with ChIP DNA Clean & Concentrator kit (Zymo). TruSeq Library Preparation Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
34159865
Reads aligned (%)
98.1
Duplicates removed (%)
6.6
Number of peaks
1595 (qval < 1E-05)

hg19

Number of total reads
34159865
Reads aligned (%)
97.8
Duplicates removed (%)
7.4
Number of peaks
1589 (qval < 1E-05)

Base call quality data from DBCLS SRA